The U.K. and Germany topped the list due to the fact that many international companies have headquarters there and their economies are appealing to hackers looking for financial gain, one expert said.
"If I'm a criminal and I'm after revenue, I want to think what countries are doing well economically," Greg Day, FireEye's chief technology officer for EMEA, told CNBC by phone.
Day added that the U.K. and Germany's maturity in identifying attacks could also have put them at the top of the pile of targeted countries.
The U.K. government classes cyberattacks as a "tier one" threat on par with terrorism. Britain's authorities have been putting in place measures to try and tackle the threat to critical infrastructure. GCHQ, the country's electronic spy agency, announced earlier this year it would share classified information with companies in an attempt to battle the threat of hackers.
The Bank of England also said it would carry out "cyber stress tests" on banks to see if they were vulnerable to attacks.
Germany has also take steps to combat cyber threats. In August, the government proposed a law to force companies to report cyberattacks.
Government services were the biggest sector targeted by hackers, followed by financial services and telecoms. These three sectors combined accounted for over 50 percent of APT attacks.